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Volumn 11, Issue , 2010, Pages

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN IMMUNOPRECIPITATION; COMPARATIVE ANALYSIS; CORRELATION ANALYSIS; EXPERIMENTAL CONDITIONS; GENETIC BACKGROUNDS; HIGH-LEVEL ANALYSIS; HIGH-THROUGHPUT TECHNOLOGIES; SYSTEMATIC ASSESSMENT;

EID: 77950898034     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-194     Document Type: Article
Times cited : (26)

References (27)
  • 2
    • 34249730556 scopus 로고    scopus 로고
    • Assessing the need for sequence-based normalization in tiling microarray experiments
    • 10.1093/bioinformatics/btm052, 17387113
    • Royce TE, Rozowsky JS, Gerstein MB. Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics 2007, 23(8):988-997. 10.1093/bioinformatics/btm052, 17387113.
    • (2007) Bioinformatics , vol.23 , Issue.8 , pp. 988-997
    • Royce, T.E.1    Rozowsky, J.S.2    Gerstein, M.B.3
  • 4
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    • 10.1038/nbt.1505, 2596672, 18978777
    • Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 2008, 26(11):1293-1300. 10.1038/nbt.1505, 2596672, 18978777.
    • (2008) Nat Biotechnol , vol.26 , Issue.11 , pp. 1293-1300
    • Ji, H.1    Jiang, H.2    Ma, W.3    Johnson, D.S.4    Myers, R.M.5    Wong, W.H.6
  • 6
    • 34447277157 scopus 로고    scopus 로고
    • Ringo-an R/Bioconductor package for analyzing ChIP-chip readouts
    • 10.1186/1471-2105-8-221, 1906858, 17594472
    • Toedling J, Skylar O, Krueger T, Fischer JJ, Sperling S, Huber W. Ringo-an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics 2007, 8:221. 10.1186/1471-2105-8-221, 1906858, 17594472.
    • (2007) BMC Bioinformatics , vol.8 , pp. 221
    • Toedling, J.1    Skylar, O.2    Krueger, T.3    Fischer, J.J.4    Sperling, S.5    Huber, W.6
  • 7
    • 67649876341 scopus 로고    scopus 로고
    • NTAP: for NimbleGen tiling array ChIP-chip data analysis
    • 10.1093/bioinformatics/btp320, 2705232, 19468055
    • He K, Li X, Zhou J, Deng XW, Zhao H, Luo J. NTAP: for NimbleGen tiling array ChIP-chip data analysis. Bioinformatics 2009, 25:1838-1840. 10.1093/bioinformatics/btp320, 2705232, 19468055.
    • (2009) Bioinformatics , vol.25 , pp. 1838-1840
    • He, K.1    Li, X.2    Zhou, J.3    Deng, X.W.4    Zhao, H.5    Luo, J.6
  • 10
    • 43349088826 scopus 로고    scopus 로고
    • XMAN: extreme MApping of OligoNucleotides
    • 10.1186/1471-2164-9-S1-S20, 2386063, 18366610
    • Li W, Carroll JS, Brown M, Liu S. xMAN: extreme MApping of OligoNucleotides. BMC Genomics 2008, 9(Suppl 1):S20. 10.1186/1471-2164-9-S1-S20, 2386063, 18366610.
    • (2008) BMC Genomics , vol.9 , Issue.SUPPL. 1
    • Li, W.1    Carroll, J.S.2    Brown, M.3    Liu, S.4
  • 12
    • 0016518897 scopus 로고
    • Efficient string matching: an aid to bibliographic search
    • Aho AV, Corasick MJ. Efficient string matching: an aid to bibliographic search. Communications of the ACM 1975, 18(36):333-340.
    • (1975) Communications of the ACM , vol.18 , Issue.36 , pp. 333-340
    • Aho, A.V.1    Corasick, M.J.2
  • 13
    • 77949576511 scopus 로고    scopus 로고
    • RMAT-an R/Bioconductor package for analyzing ChIP-chip experiments
    • 10.1093/bioinformatics/btq023, 20089513
    • Droit A, Cheung C, Gottardo R. rMAT-an R/Bioconductor package for analyzing ChIP-chip experiments. Bioinformatics 2010, 26(5):678-679. 10.1093/bioinformatics/btq023, 20089513.
    • (2010) Bioinformatics , vol.26 , Issue.5 , pp. 678-679
    • Droit, A.1    Cheung, C.2    Gottardo, R.3
  • 14
    • 24044522270 scopus 로고    scopus 로고
    • BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
    • 10.1093/bioinformatics/bti525, 16082012
    • Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 2005, 21(16):3439-3440. 10.1093/bioinformatics/bti525, 16082012.
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3439-3440
    • Durinck, S.1    Moreau, Y.2    Kasprzyk, A.3    Davis, S.4    De Moor, B.5    Brazma, A.6    Huber, W.7
  • 16
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • 10.1016/j.ygeno.2003.11.004, 14986705
    • Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 2004, 83(3):349-360. 10.1016/j.ygeno.2003.11.004, 14986705.
    • (2004) Genomics , vol.83 , Issue.3 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 17
    • 67949091194 scopus 로고    scopus 로고
    • Comparison of sequence-dependent tiling array normalization approaches
    • 10.1186/1471-2105-10-204, 2753852, 19566918
    • Chung HR, Vingron M. Comparison of sequence-dependent tiling array normalization approaches. BMC Bioinformatics 2009, 10:204. 10.1186/1471-2105-10-204, 2753852, 19566918.
    • (2009) BMC Bioinformatics , vol.10 , pp. 204
    • Chung, H.R.1    Vingron, M.2
  • 19
    • 69849089440 scopus 로고    scopus 로고
    • TileProbe: modeling tiling array probe effects using publicly available data
    • 10.1093/bioinformatics/btp425, 2735670, 19592393
    • Judy JT, Ji H. TileProbe: modeling tiling array probe effects using publicly available data. Bioinformatics 2009, 25:2369-2375. 10.1093/bioinformatics/btp425, 2735670, 19592393.
    • (2009) Bioinformatics , vol.25 , pp. 2369-2375
    • Judy, J.T.1    Ji, H.2
  • 20
    • 57149119266 scopus 로고    scopus 로고
    • Analyzing ChIP-chip data using Bioconductor
    • 10.1371/journal.pcbi.1000227, 2582686, 19043553
    • Toedling J, Huber W. Analyzing ChIP-chip data using Bioconductor. PLoS Computational Biology 2008, 4(11). 10.1371/journal.pcbi.1000227, 2582686, 19043553.
    • (2008) PLoS Computational Biology , vol.4 , Issue.11
    • Toedling, J.1    Huber, W.2
  • 21
    • 33750342702 scopus 로고    scopus 로고
    • Chromatin-immunoprecipitation and high-density tiling microarrays: a generative model, methods for analysis, and methodology assessment in the absence of a gold standard
    • University of California Berkeley, Berkeley, California, United States of America
    • Bourgon R. Chromatin-immunoprecipitation and high-density tiling microarrays: a generative model, methods for analysis, and methodology assessment in the absence of a gold standard. PhD thesis 2006, University of California Berkeley, Berkeley, California, United States of America.
    • (2006) PhD thesis
    • Bourgon, R.1
  • 22
    • 33747874899 scopus 로고    scopus 로고
    • Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays
    • 10.1016/S0076-6879(06)11014-9, 16939795
    • Scacheri PC, Crawford GE, Davis S. Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Methods Enzymol 2006, 411:270-282. 10.1016/S0076-6879(06)11014-9, 16939795.
    • (2006) Methods Enzymol , vol.411 , pp. 270-282
    • Scacheri, P.C.1    Crawford, G.E.2    Davis, S.3
  • 23
    • 43749122090 scopus 로고    scopus 로고
    • A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments
    • 10.1111/j.1541-0420.2007.00899.x, 17888037
    • Gottardo R, Li W, Johnson WE, Liu XS. A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments. Biometrics 2008, 64(2):468-478. 10.1111/j.1541-0420.2007.00899.x, 17888037.
    • (2008) Biometrics , vol.64 , Issue.2 , pp. 468-478
    • Gottardo, R.1    Li, W.2    Johnson, W.E.3    Liu, X.S.4
  • 24
    • 40549114662 scopus 로고    scopus 로고
    • CMARRT: A tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure
    • Kuan PF, Chun H, Keles S. CMARRT: A tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure. Proc. Pacific Symposium of Biocomputing 2008, (13):515-526.
    • (2008) Proc. Pacific Symposium of Biocomputing , Issue.13 , pp. 515-526
    • Kuan, P.F.1    Chun, H.2    Keles, S.3
  • 25
    • 65449150131 scopus 로고    scopus 로고
    • Structure and in vivo requirement of the yeast Spt6 SH2 domain
    • 10.1016/j.jmb.2009.04.016, 19371747
    • Dengl S, Mayer A, Sun M, Cramer P. Structure and in vivo requirement of the yeast Spt6 SH2 domain. J Mol Biol 2009, 389:211-225. 10.1016/j.jmb.2009.04.016, 19371747.
    • (2009) J Mol Biol , vol.389 , pp. 211-225
    • Dengl, S.1    Mayer, A.2    Sun, M.3    Cramer, P.4
  • 27
    • 60349122111 scopus 로고    scopus 로고
    • A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome
    • 10.1101/gr.084970.108, 2661807, 19124666
    • Venters BJ, Pugh BF. A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res 2009, 19(3):360-371. 10.1101/gr.084970.108, 2661807, 19124666.
    • (2009) Genome Res , vol.19 , Issue.3 , pp. 360-371
    • Venters, B.J.1    Pugh, B.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.